9NWW | pdb_00009nww

Single-particle cryo-EM structure of the first variant of mobilized colistin resistance (MCR-1) in its ligand-bound state

• PDB DOI: https://doi.org/10.2210/pdb9NWW/pdb
• EM Map EMD-49896: EMDB EMDataResource

• Classification: TRANSFERASE
• Organism(s): Escherichia coli, Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): No 


• Deposited: 2025-03-24 Released: 2025-12-17 
• Deposition Author(s): Zinkle, A.P., Bunuro-Batista, M., Herrera, C.M., Erramilli, S.K., Kloss, B., Ashraf, K.U., Nosol, K., Zhang, G., Cater, R.J., Marty, M.T., Kossiakoff, A.A., Trent, M.S., Nygaard, R., Stansfeld, P.J., Mancia, F.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.58 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Mechanistic basis of antimicrobial resistance mediated by the phosphoethanolamine transferase MCR-1.

Zinkle, A.P., Batista, M.B., Herrera, C.M., Erramilli, S.K., Kloss, B., Ashraf, K.U., Nosol, K., Zhang, G., Cater, R.J., Marty, M.T., Kossiakoff, A.A., Trent, M.S., Nygaard, R., Stansfeld, P.J., Mancia, F.

(2025) Nat Commun 16: 10516-10516

• PubMed: 41298376 
• DOI: https://doi.org/10.1038/s41467-025-65515-3
• Primary Citation of Related Structures:  
  9NWW


• PubMed Abstract: 
  

  Polymyxins are used to treat infections caused by multidrug-resistant Gram-negative bacteria. They are cationic peptides that target the negatively charged lipid A component of lipopolysaccharides, disrupting the outer membrane and lysing the cell. Polymyxin resistance is conferred by inner-membrane enzymes, such as phosphoethanolamine transferases, which add positively charged phosphoethanolamine to lipid A. Here, we present the structure of MCR-1, a plasmid-encoded phosphoethanolamine transferase, in its liganded form. The phosphatidylethanolamine donor substrate is bound near the active site in the periplasmic domain, and lipid A is bound over 20 Å away, within the transmembrane region. Integrating structural, biochemical, and drug-resistance data with computational analyses, we propose a two-state model in which the periplasmic domain rotates to bring the active site to lipid A, near the preferential phosphate modification site for MCR-1. This enzymatic mechanism may be generally applicable to other phosphoform transferases with large, globular soluble domains.

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Organizational Affiliation: 
• Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA.
School of Life Sciences and Department of Chemistry, University of Warwick, Coventry, UK.
Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA.
Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.
Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA.
Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia.
Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA. [e-mail].
Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA. [e-mail].
Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA. [e-mail].
School of Life Sciences and Department of Chemistry, University of Warwick, Coventry, UK. [e-mail].
Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 115.28 kDa 
• Atom Count: 6,047 
• Modeled Residue Count: 753 
• Deposited Residue Count: 1,026 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable phosphatidylethanolamine transferase Mcr-1	A [auth B]	577	Escherichia coli	Mutation(s): 0  Gene Names: mcr1, mcr-1, APZ14_31440 EC: 2.7 (PDB Primary Data), 2.7.8.43 (UniProt)
UniProt
Find proteins for A0A0R6L508 (Escherichia coli) Explore A0A0R6L508  Go to UniProtKB:  A0A0R6L508

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab (MR6) Light (L) Chain	B [auth C]	214	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab (MR6) Heavy (H) Chain	C [auth D]	235	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KDL (Subject of Investigation/LOI)	D [auth B]	(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-carboxy-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[(3~{R})-3-dodecanoyloxytetradecanoyl]amino]-6-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-3-oxidanyl-5-[[(3~{R})-3-oxidanyltetradecanoyl]amino]-4-[(3~{R})-3-oxidanyltetradecanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-4-[(3~{R})-3-tetradecanoyloxytetradecanoyl]oxy-oxan-2-yl]methoxy]-5-oxidanyl-oxan-4-yl]oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid C110 H202 N2 O39 P2 DIXUKJUHGLIZGU-OIPVZEHTSA-N
PEE (Subject of Investigation/LOI)	E [auth B]	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine C41 H78 N O8 P MWRBNPKJOOWZPW-NYVOMTAGSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.58 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-17 
Deposition Author(s): Zinkle, A.P., Bunuro-Batista, M., Herrera, C.M., Erramilli, S.K., Kloss, B., Ashraf, K.U., Nosol, K., Zhang, G., Cater, R.J., Marty, M.T., Kossiakoff, A.A., Trent, M.S., Nygaard, R., Stansfeld, P.J., Mancia, F.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM132120
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI181556
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI74416
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI176776
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI150098

Revision History  

• Version 1.0: 2025-12-17
  Type: Initial release